How To Get Domain Name Or Family Name Of A Interpro Domain Using Ipr Id

Question

[Prakki Rama]

Hi all,

I have a list of IPR id's obtained from Interpro database (eg: IPR027417, IPR000276). Now i want to find the domain name or family name of each ID at one go. Is there any better way to do it, rather than pasting each ID and retrieving info?

Thanks in advance for your suggestions.

Answer 1

[DoubleDecker]

I believe you are looking for Biomart: you can upload a list of identifiers, select what type of information you want to retrieve from the database and download the bulk results: http://central.biomart.org/martwizard/#!/Protein_sequence_and_structure?mart=InterPro (EBI, UK)

[Prakki Rama]

this was what i was looking for. Thank you DD

Answer 2

[Hamish]

The are a number of options for retrieving information from InterPro, for example:

• InterPro web site
• InterPro BioMart
• InterPro FTP site
• EBI Search
• EMBL-EBI dbfetch
• EMBL-EBI WSDbfetch
• Public SRS servers
• MRS

Most of these provide web services interfaces, which can be used to perform queries and retrieve data, so you could script against these to get the relevant information.

For example using the InterPro identifiers you mentioned (IPR027417 and IPR000276):

A. Using the EBI Search web services (EB-eye) and one of the provided sample clients to fetch the relevant fields:

$ ./ebeye_soaplite.pl --getResults interpro 'id:IPR027417 OR id:IPR000276' 'id,type,name' 0 100
IPR027417
Domain
P-loop containing nucleoside triphosphate hydrolase
IPR000276
Family
G protein-coupled receptor, rhodopsin-like

B. Using dbfetch and wget, to get a tab-delimited summary table:

$ wget -q -O - 'http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/interpro/IPR027417,IPR000276/tab'
#InterPro 43.1 25-JUL-13
#Id    Type    Short_name    Name
IPR027417    Domain    P-loop_NTPase    P-loop containing nucleoside triphosphate hydrolase
IPR000276    Family    GPCR_Rhodpsn    G protein-coupled receptor, rhodopsin-like

C. Using WSDbfetch and one of the provided sample clients to fetch a tab-delimited summary table given a list of InterPro identifiers in a file:

$ ./wsdbfetch_soaplite.pl fetchBatch interpro @interpro_id_list.txt tab raw
#InterPro 43.1 25-JUL-13
#Id    Type    Short_name    Name
IPR027417    Domain    P-loop_NTPase    P-loop containing nucleoside triphosphate hydrolase
IPR000276    Family    GPCR_Rhodpsn    G protein-coupled receptor, rhodopsin-like

Alternatively the summary information available in files on the InterPro FTP site:

• entry.list
• names.dat
• short_names.dat

Might be a good place to get the information you need... The 'names.dat' and 'short_names.dat' files contain simple tab-delimited tables giving the InterPro identifier and the entry name or short name. As such you can look-up the names by greping the file with your identifier(s), import the data into a spreadsheet or database and run queries to get the mapping, or index the file and use the index to perform look-ups. The 'entry.list' file is a little more complex from a formatting perspective since is categorizes the InterPro entries according to their type.

[Prakki Rama]

Thank you hamish. I will consider it.